This is a working document for all the coral physiology data manipulation, analysis, and visualization of the physiology manuscript. The document includes all figures, tables, supplemental materials, methods, and results for the manuscript. Each major analysis is separated by the tabs on the left.



Principal component analyses

Methods:

Principal component analysis (PCA) (function prcomp) of scaled and centered physiological parameters (host carbohydrate, host lipid, host protein, algal symbiont chlorophyll a, algal symbiont cell density, holobiont calcification rate as previously for the same samples in Bove et al (2019)) were employed to assess the relationship between physiological parameters and treatment conditions for each coral species. Main effects (temperature, pCO2, reef environment) were evaluated with PERMANOVA using the adonis2 function (vegan package; version 2.5.7 (Oksanen et al., 2020)).


Siderastrea siderea

## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 1500
## 
## adonis2(formula = sid_pca_df ~ fpco2 + ftemp + reef, data = s_df, permutations = bootnum, method = "eu")
##          Df SumOfSqs      R2      F    Pr(>F)    
## fpco2     3    61072 0.20845 8.1535 0.0006662 ***
## ftemp     1     7471 0.02550 2.9922 0.0912725 .  
## reef      1    24705 0.08432 9.8948 0.0013324 ** 
## Residual 80   199740 0.68174                     
## Total    85   292988 1.00000                     
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1



Pseudodiploria strigosa

## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 1500
## 
## adonis2(formula = dip_pca_df ~ reef + ftemp + fpco2, data = p_df, permutations = bootnum, method = "eu")
##          Df SumOfSqs      R2       F    Pr(>F)    
## reef      1    97850 0.08659 14.2890 0.0006662 ***
## ftemp     1   515604 0.45625 75.2935 0.0006662 ***
## fpco2     3    30444 0.02694  1.4819 0.2365090    
## Residual 71   486202 0.43023                      
## Total    76  1130099 1.00000                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1



Porites astreoides

## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 1500
## 
## adonis2(formula = por_pca_df ~ reef + ftemp + fpco2, data = a_df, permutations = bootnum, method = "eu")
##          Df SumOfSqs      R2       F    Pr(>F)    
## reef      1      157 0.00111  0.1138 0.7415057    
## ftemp     1    25414 0.17971 18.4700 0.0006662 ***
## fpco2     3    30537 0.21594  7.3978 0.0006662 ***
## Residual 62    85309 0.60325                      
## Total    67   141417 1.00000                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1



Figure 1

Figure 1. Principal component analysis (PCA) of all coral holobiont physiological parameters for (A) S. siderea, (B) P. strigosa, and (C) P. astreoides after 93 days of exposure to different temperature and pCO2 treatments. PCAs in the top row are depicted by temperature treatment for each species (28\(^\circ\)C blue; 31\(^\circ\)C red) and the bottom row of PCAs are depicted by pCO2 for each species (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.



Figure 4

## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 1500
## 
## adonis2(formula = all_pca_df ~ fpco2 + ftemp + reef + species + ftemp:species + fpco2:species + reef:species, data = all_df, permutations = bootnum, method = "eu")
##                Df SumOfSqs      R2        F    Pr(>F)    
## fpco2           3   149393 0.03848   8.2405 0.0006662 ***
## ftemp           1    17313 0.00446   2.8650 0.0932712 .  
## reef            1    58058 0.01496   9.6075 0.0046636 ** 
## species         2  1642613 0.42313 135.9102 0.0006662 ***
## ftemp:species   2   553351 0.14254  45.7844 0.0006662 ***
## fpco2:species   6    90865 0.02341   2.5061 0.0239840 *  
## reef:species    2    77259 0.01990   6.3924 0.0039973 ** 
## Residual      214  1293204 0.33312                       
## Total         231  3882055 1.00000                       
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Figure 4. Principal component analysis (PCA) comparing the coral holobiont of all three species at the end of the experiment depicted by (A) species, (B) pCO2 treatment, and (C) temperature treatment. Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.



Results

Principal component analysis

Two principal components (PCs) explained approximately 66% of the variance in physiological responses of the S. siderea holobiont to ocean acidification and warming treatments (Figure 1A). PC1 was driven by differences in algal symbiont physiology (chlorophyll a, cell density), while PC2 represented an inverse relationship between host energy reserves (lipid, protein, carbohydrate) and calcification rates and color intensities. Overall, lower pCO2 and temperature resulted in higher S. siderea holobiont physiology (Figure 1A). Treatment pCO2 predominantly drove S. siderea physiological responses (p = 7e-04; Table S2), while temperature and reef environment did not explain as much variation in physiological responses (p = 0.09 and p = 0.001, respectively; Table S2; Figure S1A).

For P. strigosa, 74% of the variance in the holobiont responses to treatments was explained by two PCs (Figure 1B). PC1 explained most of the variation of physiological parameters with the exception of host lipid content, which was represented in PC2. Holobiont physiology of P. strigosa was reduced under warming (p = 7e-04; Table S2) and in offshore samples (p = 7e-04; Table S2; Figure S1B), however, pCO2 did not clearly impact holobiont physiology (Figure 1B; p = 0.2; Table S2).

For P. astreoides, the first two PCs explained about 59% of the total variance in holobiont response to treatment (Figure 1C). Samples separated most clearly along PC1 driven primarily by calcification rate and algal symbiont density, while PC2 exhibited an inverse relationship between host total carbohydrate and color intensity. Overall, lower pCO2 drove higher P. astreoides holobiont physiology, while elevated temperature resulted in greater holobiont physiology (Figure 1C). Temperature (p = 7e-04; Table S2) and pCO2 (p = 7e-04; Table S2) clearly altered P. astreoides holobiont physiology, while reef environment was not significant (p = 0.7; Table S2; Figure S1C).


Species differences in coral holobiont physiology

The first two PCs of the combined holobiont physiology explained about 62% of the total variance across samples (Figure 4). In general, fragments of S. siderea contained higher chlorophyll a content, host carbohydrate, and host lipid content, while P. strigosa fragments typically had greater host protein content accompanied by higher calcification rates, and fragments of P. astreoides were differentiated by their high symbiont densities (Figure 4A; Table S5). Despite being different coral species, coral holobiont physiology exhibited similar physiological responses to pCO2 and temperature treatments (Figure 4B, 4C; Table S5). As pCO2 or temperature increased, coral holobiont physiology was more constrained and exhibited convergent physiological responses under stress. Furthermore, corals from the inshore reef environment exhibited more constrained physiology than their offshore counterparts (Figure S7; Table S5).



Correlation assessments

Methods:

Correlations of all physiological parameters were assessed to determine the relationships between parameters within each species. The Pearson correlation coefficient (R2) of each comparison was calculated using the corrgram package (version 1.13 (Wright, 2018)) and the significance was calculated using the cor.test function. These relationships were then visualized through simple scatterplots.


Figure 2

Figure 2. Coral holobiont physiological parameter scatter plots (top) and correlation matrices (bottom) for (A) S. siderea, (B) P. strigosa, and (C) P. astreoides showing pairwise comparisons of within each species. Scatter plots of each pairwise combination of physiological parameters are displayed on the top with temperature treatment depicted by shape (28\(^\circ\)C closed points; 31\(^\circ\)C open points) and pCO2 treatment depicted by color (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange). Strengths of the correlations (R2 via Pearson correlation coefficients) between each pairwise combination of physiological parameters are indicated by darker shades of blue on the bottom with significance depicted by asterisks according to significance level (* p < 0.05; ** p < 0.01; *** p < 0.001). R2 and significance levels correspond to the scatter plot at the intersection between two physiological parameters.



Results

Correlations of physiological parameters

Coral holobiont physiological parameters were generally positively correlated with one another within each of the three species. Correlations between S. siderea holobiont physiological parameters identified 15 significant relationships out of all 21 possible comparisons (Figure 2A). Of those significant correlations, six resulted in a Pearson’s correlation coefficient (R2) equal to or greater than 0.5, with the strongest relationship identified between symbiont density and chlorophyll a (R2 = 0.72).

All pairwise physiological parameters were significantly correlated with one another in P. strigosa and, of those, 15 correlations exhibit moderate (R2 > 0.50) positive relationships (Figure 2B). Notably, the two strongest correlations were host carbohydrate vs. host protein (R2 = 0.70) and host carbohydrate vs. chlorophyll a (R2 = 0.76).

Compared to both S. siderea and P. strigosa, fewer physiological traits were significantly (p < 0.05) correlated with one another in P. astreoides (12 significant out of 21 total comparisons; Figure 2C). Of the significant correlations, only two pairwise comparisons resulted in a Pearson’s correlation coefficient greater than 0.5: chlorophyll a vs. color intensity (R2 = 0.57) and host carbohydrate vs. host protein (R2 = 0.68).



Plasticity analyses

Methods:

Physiological plasticity of each experimental fragment was calculated for each species using all seven PCs calculated above as the distance between an experimental fragment and the control (420 \(\mu\)atm; 28\(^\circ\)C) fragment from that same colony. The effects of treatment (pCO2 and temperature) and natal reef environment on calculated distances were assessed using generalized linear mixed effects models (function lmer) with a Gamma distribution and log-link and a random effect for colony. The best-fit model was selected as the model with the lowest AIC for each species (Table S1). Natal reef environment was only a significant predictor of plasticity in S. siderea so samples were pooled across reef environments for both P. strigosa and P. astreoides. Parametric bootstraps were performed to model mean response and 95% confidence intervals with 1500 iterations and significant effects were identified as non-overlapping confidence intervals. Marginal and conditional R2 values were calculated using the r2_nakagawa function in the rcompanion package (version 2.4.1 (Mangiafico, 2021)). All figures and statistical analyses were carried out in R version 3.6.3 (R Core Team, 2018) and the accompanying data and code can be freely accessed on GitHub (github.com/seabove7/Bove_CoralPhysiology) and Zenodo (DOI here when close to finished).


Siderastrea siderea

## Generalized linear mixed model fit by maximum likelihood (Laplace
##   Approximation) [glmerMod]
##  Family: Gamma  ( log )
## Formula: dist ~ reef * fpco2 + ftemp + (1 | colony)
##    Data: sid_dist
## 
##      AIC      BIC   logLik deviance df.resid 
##    218.8    243.5    -98.4    196.8       59 
## 
## Scaled residuals: 
##      Min       1Q   Median       3Q      Max 
## -1.99957 -0.62958 -0.09185  0.40989  2.93911 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  colony   (Intercept) 0.03567  0.1889  
##  Residual             0.09609  0.3100  
## Number of obs: 70, groups:  colony, 11
## 
## Fixed effects:
##                  Estimate Std. Error t value Pr(>|z|)    
## (Intercept)      1.085047   0.172255   6.299 2.99e-10 ***
## reefN           -0.058293   0.247860  -0.235  0.81406    
## fpco2420         0.334631   0.172672   1.938  0.05263 .  
## fpco2680         0.209598   0.130838   1.602  0.10916    
## fpco23290        0.418697   0.132009   3.172  0.00152 ** 
## ftemp31          0.003138   0.076026   0.041  0.96708    
## reefN:fpco2420  -0.703806   0.238723  -2.948  0.00320 ** 
## reefN:fpco2680  -0.409193   0.196622  -2.081  0.03742 *  
## reefN:fpco23290 -0.278200   0.191371  -1.454  0.14602    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Correlation of Fixed Effects:
##             (Intr) reefN  fp2420 fp2680 f23290 ftmp31 rN:242 rN:268
## reefN       -0.671                                                 
## fpco2420    -0.304  0.252                                          
## fpco2680    -0.459  0.325  0.468                                   
## fpco23290   -0.446  0.320  0.475  0.611                            
## ftemp31     -0.159 -0.038 -0.275 -0.041 -0.069                     
## rfN:fpc2420  0.244 -0.352 -0.678 -0.331 -0.331  0.034              
## rfN:fpc2680  0.310 -0.438 -0.303 -0.664 -0.404 -0.004  0.456       
## rfN:fp23290  0.309 -0.449 -0.324 -0.421 -0.689  0.035  0.466  0.572
## # R2 for Mixed Models
## 
##   Conditional R2: 0.506
##      Marginal R2: 0.322



Pseudodiploria strigosa

## Generalized linear mixed model fit by maximum likelihood (Laplace
##   Approximation) [glmerMod]
##  Family: Gamma  ( log )
## Formula: dist ~ fpco2 + ftemp + (1 | colony)
##    Data: dip_dist
## 
##      AIC      BIC   logLik deviance df.resid 
##     97.5    104.8    -42.7     85.5       19 
## 
## Scaled residuals: 
##      Min       1Q   Median       3Q      Max 
## -1.70079 -0.72697  0.05779  0.77668  2.01138 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  colony   (Intercept) 0.007898 0.08887 
##  Residual             0.137879 0.37132 
## Number of obs: 25, groups:  colony, 5
## 
## Fixed effects:
##             Estimate Std. Error t value Pr(>|z|)    
## (Intercept)  1.27912    0.14767   8.662   <2e-16 ***
## fpco2680    -0.33844    0.19338  -1.750   0.0801 .  
## fpco23290   -0.05892    0.18739  -0.314   0.7532    
## ftemp31      0.22671    0.17289   1.311   0.1898    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Correlation of Fixed Effects:
##           (Intr) fp2680 f23290
## fpco2680  -0.579              
## fpco23290 -0.578  0.484       
## ftemp31   -0.334  0.066  0.012
## # R2 for Mixed Models
## 
##   Conditional R2: 0.232
##      Marginal R2: 0.188



Porites astreoides

## Generalized linear mixed model fit by maximum likelihood (Laplace
##   Approximation) [glmerMod]
##  Family: Gamma  ( log )
## Formula: dist ~ fpco2 + ftemp + (1 | colony)
##    Data: por_dist
## 
##      AIC      BIC   logLik deviance df.resid 
##    140.4    154.4    -63.2    126.4       47 
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -1.6588 -0.5857 -0.1014  0.5424  2.2086 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  colony   (Intercept) 0.03732  0.1932  
##  Residual             0.05675  0.2382  
## Number of obs: 54, groups:  colony, 11
## 
## Fixed effects:
##             Estimate Std. Error t value Pr(>|z|)    
## (Intercept)  1.03836    0.12055   8.613  < 2e-16 ***
## fpco2420    -0.04691    0.11022  -0.426    0.670    
## fpco2680     0.03247    0.07465   0.435    0.664    
## fpco23290    0.12169    0.07752   1.570    0.116    
## ftemp31      0.26414    0.06483   4.074 4.62e-05 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Correlation of Fixed Effects:
##           (Intr) fp2420 fp2680 f23290
## fpco2420  -0.138                     
## fpco2680  -0.313  0.383              
## fpco23290 -0.330  0.294  0.529       
## ftemp31   -0.176 -0.379 -0.087  0.089
## # R2 for Mixed Models
## 
##   Conditional R2: 0.485
##      Marginal R2: 0.147



Figure 3

Figure 3. Holobiont physiological plasticity of (A) S. siderea, (B) P. strigosa, and (C) P. astreoides after 93-day exposure to experimental treatments. Higher values represent greater plasticity in coral holobiont samples. Natal reef environment is depicted along the x axis for S. siderea, however, P. strigosa and and P. astreoides samples were pooled by reef environment. pCO2 treatment is depicted by color and shape (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange) and temperature is represented as either closed (28 \(^\circ\)C) or open (31 \(^\circ\)C) symbols. Symbols and bars indicate modeled means and 95% confidence intervals.



Results

Coral holobiont physiological plasticity

Physiological plasticity of offshore S. siderea fragments exhibited a positive linear trend with increasing pCO2 while the inshore fragments appear to respond in a parabolic pattern to pCO2, with the lowest calculated distances occurring at 420 \(\mu\)atm, 31\(^\circ\)C and 680 \(\mu\)atm, 28\(^\circ\)C (Figure 3A). Further, offshore S. siderea fragments exhibited higher plasticity in the extreme pCO2 treatment than in inshore fragments reared in the pre-industrial, current-day, and extreme pCO2 treatments, regardless of temperature (Figure 3A; Table S3). Plasticity of P. strigosa and P. astreoides was not clearly different between colonies based on natal reef environments (see Table S1). No clear differences in physiological plasticity in response to treatment were identified in P.strigosa (Figure 3B; Table S3), however, this is likely due to reduced sample sizes in this analysis as a result of only five colonies (Noffshore = 3, Ninshore = 2) present in the control treatment for distance calculations. Elevated temperatures generally resulted in higher plasticity of P. astreoides compared to control temperatures (Figure 3C; Table S3), however, this trend was not clearly different within each pCO2 treatment. Physiological plasticity of P. astreoides was significantly lower in both the pre-industrial and end-of-century pCO2 treatments at control temperatures than that measured in the extreme pCO2 treatment combined with the elevated temperature.



Supplemental Figures

Figure S1

Figure S1. Principal component analysis (PCA) of all coral holobiont physiological parameters for (A) S. siderea, (B) P. strigosa, and (C) P. astreoides depicted by natal reef environment (offshore green; inshore yellow). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.



Figure S2

Figure S2. Principal component analysis (PCA) of S. siderea coral host (protein, lipid, carbohydrate; left) or algal symbiont (chlorophyll a, symbiont density, color intensity; right) physiological parameters by temperature (28\(^\circ\)C blue; 31\(^\circ\)C red), pCO2 (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange), and natal reef environment (offshore green; inshore yellow). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.



Figure S3

Figure S3. Principal component analysis (PCA) of P. strigosa coral host (protein, lipid, carbohydrate; left) or algal symbiont (chlorophyll a, symbiont density, color intensity; right) physiological parameters by temperature (28\(^\circ\)C blue; 31\(^\circ\)C red), pCO2 (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange), and natal reef environment (offshore green; inshore yellow). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.



Figure S4

Figure S4. Principal component analysis (PCA) of P. asteroides coral host (protein, lipid, carbohydrate; left) or algal symbiont (chlorophyll a, symbiont density, color intensity; right) physiological parameters by temperature (28\(^\circ\)C blue; 31\(^\circ\)C red), pCO2 (pre industrial [300 \(\mu\)atm], light purple; current day [420 \(\mu\)atm], dark purple; end-of-century [680 \(\mu\)atm], light orange; extreme [3290 \(\mu\)atm], dark orange), and natal reef environment (offshore green; inshore yellow). Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.



Figure S5

Figure S5. Coral host vs. algal symbiont physiological plasticity of (A) S. siderea, (B) P. strigosa, and (C) P. astreoides after 93-day exposure to experimental treatments. Higher values represent greater plasticity in coral holobiont samples. pCO2 treatment is depicted by color and shape (pre industrial [300 μatm], light purple; current day [420 μatm], dark purple; end-of-century [680 μatm], light orange; extreme [3290 μatm], dark orange) and temperature is represented as either closed (28 °C) or open (31 °C) symbols. Symbols and bars indicate modeled means and 95% confidence intervals.



Figure S6

Figure S6. Mean (\(\pm\)SE) physiological parameter (each row) measured for (A) S. siderea, (B) P. strigosa, (C) P. astreoides, and (D) U. tenuifolia at the completion of the 93-day experimental period. pCO2 treatment is represented along the x axis and the temperature is depicted by color (28\(^\circ\)C blue; 31\(^\circ\)C red).



Figure S7

Figure S7. Coral color changes over the experimental period. Representative images of fragments of (A) P. astreoides, (B) S. siderea, and (C) P. strigosa from the same colonies demonstrating change in coral color over time in either control (420 μatm; 28 °C) or warming (420 μatm; 31 °C) treatments from the start of the experiment (T0) to the end (T90).



Figure S8

Figure S8. Principal component analysis (PCA) comparing the coral holobiont of all three species at the end of the experiment depicted reef environment. Arrows represent significant (p < 0.05) correlation vectors for physiological parameters and ellipses represent 95% confidence based on multivariate t-distributions.



Supplemental Tables

Table S1

Table S1. Model performance comparisons of generalized linear mixed effects models (GLMM) for plasticity assessments to select the best-fit model per species using the package performance (version 0.7.0). Akaike information criterion (AIC) was used to select the best-fit model per species. The performance score computes indices of model performance for all models per species at once for comparison across models. The models highlighted in grey were used for bootstrapping estimates and 95% confidence intervals.
Model formula AIC BIC Conditional R2 Marginal R2
Siderastrea Siderea
reef environment * pCO2 + temperature + (1 | colony) 218.8 243.5 0.506 0.322
reef environment * pCO2 * temperature + (1 | colony) 223.2 259.2 0.545 0.366
reef environment * (pCO2 + temperature) + (1 | colony) 220.1 247.1 0.512 0.329
reef environment + pCO2 + temperature + (1 | colony) 221.6 239.6 0.442 0.254
pCO2 + temperature + (1 | colony) 222.1 237.8 0.370 0.088
reef environment + pCO2 * temperature + (1 | colony) 225.6 248.1 0.442 0.253
Pseudodiploria strigosa
reef environment * pCO2 * temperature + (1 | colony) 105.6 121.5 0.397 0.317
reef environment * pCO2 + temperature + (1 | colony) 100.8 111.8 0.309 0.261
reef environment + pCO2 * temperature + (1 | colony) 101.6 112.6 0.278 0.238
pCO2 + temperature + (1 | colony) 97.5 104.8 0.232 0.188
Porites astreoides
reef environment * pCO2 + temperature + (1 | colony) 145.9 167.8 0.521 0.195
reef environment * (pCO2 + temperature) + (1 | colony) 147.9 171.8 0.522 0.195
reef environment * pCO2 * temperature + (1 | colony) 153.1 182.9 0.527 0.199
reef environment + pCO2 + temperature + (1 | colony) 142.3 158.2 0.499 0.174
pCO2 + temperature + (1 | colony) 140.4 154.4 0.485 0.147
reef environment + pCO2 * temperature + (1 | colony) 146.2 166.1 0.500 0.174




Table S2

Table S2. PERMANOVA model output from each species using the adonis2 function with 1500 iterations.
Df Sum of Squares R2 F P-value
Siderastrea Siderea
pCO2 3 61072 0.208 8.15 0.00067
temperature 1 7471 0.025 2.99 0.09127
reef environment 1 24705 0.084 9.89 0.00133
Residual 80 199740 0.682
Total 85 292988 1.000
Pseudodiploria strigosa
reef environment 1 97850 0.087 14.29 0.00067
temperature 1 515604 0.456 75.29 0.00067
pCO2 3 30444 0.027 1.48 0.23651
Residual 71 486202 0.430
Total 76 1130099 1.000
Porites astreoides
reef environment 1 157 0.001 0.11 0.74151
temperature 1 25414 0.180 18.47 0.00067
pCO2 3 30537 0.216 7.40 0.00067
Residual 62 85309 0.603
Total 67 141417 1.000




Table S3

Table S3. GLMM output from plasticity assessments for each species. The intercept of each model was set as 300 \(\mu\)atm, 28\(^\circ\)C, and inshore reef environment.
Estimate Standard error Statistic P-value
Siderastrea Siderea
(Intercept) 1.085 0.172 6.30 0.000
reef environment (offshore) -0.058 0.248 -0.24 0.814
pCO2-current 0.335 0.173 1.94 0.053
pCO2-EOC 0.210 0.131 1.60 0.109
pCO2-extreme 0.419 0.132 3.17 0.002
temperature (31C) 0.003 0.076 0.04 0.967
reef environment (offshore):pCO2-current -0.704 0.239 -2.95 0.003
reef environment (offshore):pCO2-EOC -0.409 0.197 -2.08 0.037
reef environment (offshore):pCO2-extreme -0.278 0.191 -1.45 0.146
Conditional R2 0.506
Marginal R2 0.322
Pseudodiploria strigosa
(Intercept) 1.279 0.148 8.66 0.000
pCO2-EOC -0.338 0.193 -1.75 0.080
pCO2-extreme -0.059 0.187 -0.31 0.753
temperature (31C) 0.227 0.173 1.31 0.190
Conditional R2 0.232
Marginal R2 0.188
Porites astreoides
(Intercept) 1.038 0.121 8.61 0.000
pCO2-current -0.047 0.110 -0.43 0.670
pCO2-EOC 0.032 0.075 0.44 0.664
pCO2-extreme 0.122 0.078 1.57 0.116
temperature (31C) 0.264 0.065 4.07 0.000
Conditional R2 0.485
Marginal R2 0.147




Table S4

Table S4. PERMANOVA model output across species using the adonis2 function with 1500 iterations.
Df Sum of Squares R2 F P-value
pCO2 3 149393 0.038 8.24 0.00067
temperature 1 17313 0.004 2.87 0.09327
reef environment 1 58058 0.015 9.61 0.00466
species 2 1642613 0.423 135.91 0.00067
temperature:species 2 553351 0.143 45.78 0.00067
pCO2:species 6 90865 0.023 2.51 0.02398
reef environment:species 2 77259 0.020 6.39 0.00400
Residual 214 1293204 0.333
Total 231 3882055 1.000




Table S5

Table S5. PERMANOVA model output of coral host or algal symbiont physiology per species using the adonis2 function with 1500 iterations depicted in Figures S2-S4.
Coral host
Algal symbionts
Df Sum of Squares R2 F P-value Df Sum of Squares R2 F P-value
Siderastrea Siderea
pCO2 3 1 0.019 0.55 0.74217 3 61056 0.208 8.15 0.00067
temperature 1 3 0.075 6.65 0.00333 1 7468 0.025 2.99 0.09927
reef environment 1 0 0.006 0.52 0.56762 1 24705 0.084 9.90 0.00200
Residual 80 30 0.901 80 199684 0.682
Total 85 34 1.000 85 292913 1.000
Pseudodiploria strigosa
pCO2 3 1 0.041 1.23 0.30513 3 26899 0.024 1.31 0.27981
temperature 1 3 0.147 13.12 0.00067 1 515173 0.456 75.24 0.00067
reef environment 1 0 0.020 1.75 0.15656 1 101793 0.090 14.87 0.00067
Residual 71 14 0.793 71 486140 0.430
Total 76 18 1.000 76 1130005 1.000
Porites astreoides
pCO2 3 2 0.136 3.48 0.01532 3 29037 0.205 7.04 0.00133
temperature 1 0 0.036 2.76 0.08195 1 26338 0.186 19.15 0.00067
reef environment 1 0 0.021 1.64 0.17988 1 724 0.005 0.53 0.47901
Residual 62 10 0.807 62 85288 0.603
Total 67 13 1.000 67 141387 1.000



Table S6

Table S6. Model performance comparisons of generalized linear mixed effects models (GLMM) for plasticity assessments to select the best-fit model comparing host and symbiont using the package performance (version 0.7.0). Akaike information criterion (AIC) was used to select the best-fit model. The performance score computes indices of model performance for all models per species at once for comparison across models. The models highlighted in grey were used for bootstrapping estimates and 95% confidence intervals.
Model formula AIC Conditional R2 Marginal R2
species * part * reef environment * pCO2 * temperature + (1 | colony) 923.1 0.430 0.318
species * part * reef environment * (pCO2 + temperature) + (1 | colony) 902.1 0.391 0.279
reef environment * species * part * (pCO2 + temperature) + (1 | colony) 902.1 0.391 0.279
reef environment * species * part * (pCO2 + temperature) + (1 | colony) 902.1 0.391 0.279
species * part * (pCO2 + temperature + reef environment) + (1 | colony) 883.9 0.323 0.213
species * part * (pCO2 + temperature) + (1 | colony) 882.0 0.280 0.139
species * part * (pCO2 + temperature) + reef environment + (1 | colony) 883.5 0.282 0.144
species * part * reef environment * pCO2 + temperature + (1 | colony) 904.6 0.338 0.225
species * part * pCO2 + temperature + (1 | colony) 890.2 0.235 0.093
species * reef environment + part + pCO2 + temperature + (1 | colony) 881.2 0.205 0.095
species * part * reef environment + pCO2 * temperature + (1 | colony) 890.2 0.222 0.113




Table S7

Table S7. GLMM output from plasticity assessments for coral host vs. algal symbiont for each species. The intercept of each model was set as coral host, S. siderea, 300 \(\mu\)atm, and 28\(^\circ\)C.
Estimate Standard error Statistic P-value
(Intercept) 0.800 0.172 4.66 0.000
PSTR 0.200 0.290 0.69 0.491
PAST -0.357 0.244 -1.47 0.143
symbionts -0.515 0.185 -2.78 0.005
pCO2-current 0.235 0.214 1.10 0.272
pCO2-EOC 0.006 0.164 0.03 0.972
pCO2-extreme -0.021 0.161 -0.13 0.896
temperature (31C) -0.252 0.128 -1.97 0.049
PSTR:symbionts 0.222 0.308 0.72 0.472
PAST:symbionts 0.685 0.270 2.54 0.011
PSTR:pCO2-current -0.088 0.592 -0.15 0.882
PAST:pCO2-current -0.569 0.339 -1.68 0.093
PSTR:pCO2-EOC -0.451 0.298 -1.51 0.131
PAST:pCO2-EOC 0.050 0.240 0.21 0.835
PSTR:pCO2-extreme -0.154 0.288 -0.54 0.592
PAST:pCO2-extreme 0.236 0.245 0.96 0.336
PSTR:temperature (31C) 0.071 0.250 0.29 0.775
PAST:temperature (31C) 0.608 0.200 3.04 0.002
symbionts:pCO2-current -0.299 0.298 -1.00 0.316
symbionts:pCO2-EOC 0.134 0.227 0.59 0.556
symbionts:pCO2-extreme 0.564 0.226 2.50 0.013
symbionts:temperature (31C) 0.524 0.181 2.89 0.004
PSTR:symbionts:pCO2-current 0.362 0.818 0.44 0.658
PAST:symbionts:pCO2-current 0.673 0.473 1.42 0.155
PSTR:symbionts:pCO2-EOC -0.177 0.418 -0.42 0.672
PAST:symbionts:pCO2-EOC -0.181 0.335 -0.54 0.590
PSTR:symbionts:pCO2-extreme -0.482 0.401 -1.20 0.229
PAST:symbionts:pCO2-extreme -0.891 0.341 -2.61 0.009
PSTR:symbionts:temperature (31C) 0.191 0.350 0.54 0.586
PAST:symbionts:temperature (31C) -0.606 0.281 -2.16 0.031
Conditional R2 0.280
Marginal R2 0.139




Session information

Session information from the last run date on 2021-06-30:

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] janitor_2.1.0         rcompanion_2.4.1      car_3.0-10           
##  [4] carData_3.0-4         png_0.1-7             MASS_7.3-53          
##  [7] performance_0.7.0     wesanderson_0.3.6     RColorBrewer_1.1-2   
## [10] gridGraphics_0.5-1    corrplot_0.84         Hmisc_4.4-2          
## [13] Formula_1.2-4         survival_3.2-7        magick_2.5.2         
## [16] ggpubr_0.4.0          vroom_1.3.2           lmerTest_3.1-3       
## [19] lme4_1.1-26           Matrix_1.3-2          kableExtra_1.3.1     
## [22] finalfit_1.0.2        ggfortify_0.4.11-9009 cowplot_1.1.1        
## [25] Rmisc_1.5             shiny_1.5.0           vegan_2.5-7          
## [28] lattice_0.20-41       permute_0.9-5         forcats_0.5.0        
## [31] stringr_1.4.0         purrr_0.3.4           tibble_3.0.4         
## [34] tidyverse_1.3.0       plotly_4.9.3          openxlsx_4.2.3       
## [37] corrgram_1.13         tidyr_1.1.2           ggbiplot_0.55        
## [40] scales_1.1.1          plyr_1.8.6            dplyr_1.0.2          
## [43] ggplot2_3.3.3         broom_0.7.3           readr_1.4.0          
## [46] knitr_1.33           
## 
## loaded via a namespace (and not attached):
##   [1] tidyselect_1.1.0    htmlwidgets_1.5.3   TSP_1.1-10         
##   [4] munsell_0.5.0       effectsize_0.4.1    codetools_0.2-18   
##   [7] statmod_1.4.35      withr_2.4.2         colorspace_2.0-0   
##  [10] highr_0.8           rstudioapi_0.13     stats4_3.6.3       
##  [13] DescTools_0.99.41   ggsignif_0.6.0      labeling_0.4.2     
##  [16] bit64_4.0.5         farver_2.0.3        vctrs_0.3.6        
##  [19] generics_0.1.0      TH.data_1.0-10      xfun_0.22          
##  [22] R6_2.5.0            seriation_1.2-9     assertthat_0.2.1   
##  [25] promises_1.1.1      multcomp_1.4-15     nnet_7.3-14        
##  [28] rootSolve_1.8.2.1   gtable_0.3.0        multcompView_0.1-8 
##  [31] lmom_2.8            sandwich_3.0-0      rlang_0.4.11       
##  [34] splines_3.6.3       rstatix_0.6.0       lazyeval_0.2.2     
##  [37] checkmate_2.0.0     yaml_2.2.1          abind_1.4-5        
##  [40] modelr_0.1.8        backports_1.2.1     httpuv_1.5.5       
##  [43] tools_3.6.3         ellipsis_0.3.1      ggridges_0.5.3     
##  [46] Rcpp_1.0.5          base64enc_0.1-3     rpart_4.1-15       
##  [49] zoo_1.8-8           haven_2.3.1         ggrepel_0.9.0      
##  [52] cluster_2.1.0       fs_1.5.0            magrittr_2.0.1     
##  [55] data.table_1.13.6   lmtest_0.9-38       reprex_0.3.0       
##  [58] mvtnorm_1.1-1       matrixStats_0.57.0  hms_1.0.0          
##  [61] mime_0.10           evaluate_0.14       xtable_1.8-4       
##  [64] rio_0.5.16          jpeg_0.1-8.1        readxl_1.3.1       
##  [67] gridExtra_2.3       compiler_3.6.3      mice_3.13.0        
##  [70] crayon_1.3.4        minqa_1.2.4         htmltools_0.5.1    
##  [73] mgcv_1.8-33         later_1.1.0.1       libcoin_1.0-8      
##  [76] expm_0.999-6        Exact_2.1           lubridate_1.7.9.2  
##  [79] DBI_1.1.0           dbplyr_2.0.0        see_0.6.2          
##  [82] boot_1.3-25         cli_2.5.0           parallel_3.6.3     
##  [85] insight_0.13.1      pkgconfig_2.0.3     registry_0.5-1     
##  [88] numDeriv_2016.8-1.1 coin_1.4-1          foreign_0.8-75     
##  [91] xml2_1.3.2          foreach_1.5.1       webshot_0.5.2      
##  [94] rvest_0.3.6         snakecase_0.11.0    digest_0.6.27      
##  [97] parameters_0.10.1   rmarkdown_2.6       cellranger_1.1.0   
## [100] htmlTable_2.1.0     nortest_1.0-4       gld_2.6.2          
## [103] curl_4.3.1          modeltools_0.2-23   nloptr_1.2.2.2     
## [106] lifecycle_1.0.0     nlme_3.1-151        jsonlite_1.7.2     
## [109] viridisLite_0.3.0   pillar_1.4.7        fastmap_1.0.1      
## [112] httr_1.4.2          glue_1.4.2          bayestestR_0.8.0   
## [115] zip_2.1.1           iterators_1.0.13    bit_4.0.4          
## [118] class_7.3-17        stringi_1.5.3       latticeExtra_0.6-29
## [121] e1071_1.7-4